Merge pull request #1590 from girder/plottable-elements

Add an index to speed up getting plottable data from annotation elements
girder · Jul 29, 2024 · 1e9a870 · 1e9a870
2 parents 8a706f0 + 94ec077
commit 1e9a870
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Showing 3 changed files with 21 additions and 7 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -6,6 +6,7 @@
 
 - Make the plottable data class threadsafe ([#1588](../../pull/1588))
 - Speed up getting plottable data from items ([#1589](../../pull/1589))
+- Add an index to speed up getting plottable data from annotation elements ([#1590](../../pull/1590))
 
 ## 1.29.4
 

diff --git a/girder_annotation/girder_large_image_annotation/models/annotationelement.py b/girder_annotation/girder_large_image_annotation/models/annotationelement.py
@@ -79,6 +79,13 @@ def initialize(self):
             ], {
                 'name': 'annotationGroupIdx',
             }),
+            ([
+                ('annotationId', SortDir.ASCENDING),
+                ('_version', SortDir.DESCENDING),
+                ('_id', SortDir.ASCENDING),
+            ], {
+                'name': 'annotationElementIdIdx',
+            }),
             ([
                 ('created', SortDir.ASCENDING),
                 ('_version', SortDir.ASCENDING),
@@ -159,6 +166,13 @@ def getElements(self, annotation, region=None):
         annotation['annotation']['elements'] = list(self.yieldElements(
             annotation, region, annotation['_elementQuery']))
 
+    def countElements(self, annotation):
+        query = {
+            'annotationId': annotation.get('_annotationId', annotation['_id']),
+            '_version': annotation['_version'],
+        }
+        return self.collection.count_documents(query)
+
     def yieldElements(self, annotation, region=None, info=None, bbox=False):  # noqa
         """
         Given an annotation, fetch the elements from the database.

diff --git a/girder_annotation/girder_large_image_annotation/utils/__init__.py b/girder_annotation/girder_large_image_annotation/utils/__init__.py
@@ -1,4 +1,3 @@
-import itertools
 import json
 import math
 import re
@@ -347,7 +346,7 @@ def isGeoJSON(annotation):
 
 class PlottableItemData:
     maxItems = 1000
-    maxAnnotationElements = 10000
+    maxAnnotationElements = 5000
     maxDistinct = 20
     allowedTypes = (str, bool, int, float)
 
@@ -878,11 +877,11 @@ def _getColumns(self):
                 if not self._sources or 'annotation' in self._sources:
                     self._collectColumns(columns, [annot], 'annotation', iid=iid)
                 # add annotation elements
-                if not self._sources or 'annotationelement' in self._sources:
-                    elements = list(itertools.islice(Annotationelement().yieldElements(
-                        annot, bbox=True), self.maxAnnotationElements))
-                    self._collectColumns(
-                        columns, elements, 'annotationelement', iid=iid, aid=str(annot['_id']))
+                if ((not self._sources or 'annotationelement' in self._sources) and
+                        Annotationelement().countElements(annot) <= self.maxAnnotationElements):
+                    for element in Annotationelement().yieldElements(annot, bbox=True):
+                        self._collectColumns(
+                            columns, [element], 'annotationelement', iid=iid, aid=str(annot['_id']))
         # TODO: Add csv
         for result in columns.values():
             if len(result['distinct']) <= self.maxDistinct: